Maxaud

(NOTE: Before saying this plugin is broken, please understand what this plugin does. It’s meant for WordPress installs that have multiple NETWORKS.)
Adds the ability to have different themes available to different NETWORKS in a multisite atmoshpere.
WordPress allows for multiple “networks”, these are not to be confused with sites. A network holds blogs underneath of it.
This plugin will allow you to separate themes into different directories so they’re only accessable and viewable to the networks you choose.
The plugin will attempt to create a directory in the /wp-content/ directory named /ms-themes/. If it fails to create it, then you will need to make one.
In the /ms-themes/ directory you will create a folder for each network that you want to allow only certain themes to.
Example: 
If you have a theme named “Snarfer Theme”, and you want to only allow it to be viewable/available to the network (and all sites on that network) with the site_id of 7, you would place the snarfer theme directory in /wp-content/ms-themes/7/
Future releases:
<ul>
<li>Network option to turn off auto creation on/off network directories, index.php files.</li>
<li>Network option to display network ID in the footer of sites so network admins can easily tell what network a site is under.</li>
</ul>

Multisite Themes

Adds the ability to have different themes available to different NETWORKS in a multisite atmoshpere.

kodeala

Reorder Multisite Sites Dropdown gives WordPress Multisite administrators a powerful tool to organize the My Sites dropdown in the WordPress Admin Bar. With this plugin, you can customize how sites appear in the admin bar so they are easier to find and better organized for your workflow. It is especially useful for WordPress Multisite networks with many sites where the default alphabetical ordering becomes difficult to manage, enhancing the existing WordPress multisite admin bar experience without modifying WordPress core functionality.
With this plugin, you can:
<ul>
<li>Reorder sites in the My Sites dropdown using drag-and-drop.</li>
<li>Manually set ordering using number input fields for quick repositioning.</li>
<li>Create groups to organize related sites together.</li>
<li>Add divider lines to visually separate sections.</li>
<li>Nest sites inside groups for better structure.</li>
</ul>
The ordering interface is available in the Network Admin under Settings > Reorder My Sites

Reorder Multisite Sites Dropdown

Adds advanced ordering controls to the WordPress Multisite My Sites admin bar dropdown, allowing administrators to organize sites with drag-and-drop,  …

Multisite Themes vs Reorder Multisite Sites Dropdown